Recent examinations of published sequences for hemagglutinin (HA) from Vietnam H5N1 strains indicate that these highly pathogenic stains are more variable than previously observed. It would therefore be unexpected for vaccines with less than 90% homology to challenge strains to be effective in controlling symptoms or reduce shedding.
We have evaluated the public record of complete amino acid sequences and found that the sequence homology of the HA1 fragment of the hemagglutinin (HA) viral protein in H5 serotypes are 100 to 83% homologous to the Turkey Wisconsin 68 Strain at the amino acid level. Recent publications by Swayne et al. (Vet Micro, 2000, 74:165-172) have shown that a fowl pox vectored HA based AIV vaccine was able to prevent infection in a heterotypic challenge experiment with strains of AIV that that contained HA1 with 87% or greater amino acid homology as compared to the immunizing vaccine. The authors conclude “That vaccines with less than 90% homology to the pathogen HA1 will most likely result in inconsistent reduction in AI challenge or field virus shedding from the respiratory tract.”